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- PDB-2w9o: Solution structure of jerdostatin from Trimeresurus jerdonii -

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Basic information

Entry
Database: PDB / ID: 2w9o
TitleSolution structure of jerdostatin from Trimeresurus jerdonii
ComponentsSHORT DISINTEGRIN JERDOSTATIN
KeywordsTOXIN / VENOM / CELL ADHESION / BLOOD COAGULATION
Function / homologyDisintegrin domain / Echistatin / Disintegrin domain superfamily / Few Secondary Structures / Irregular / toxin activity / extracellular region / Disintegrin jerdostatin
Function and homology information
Biological speciesTRIMERESURUS JERDONII (snake)
MethodSOLUTION NMR / CNS
AuthorsCarbajo, R.J. / Sanz, L. / Mosulen, S. / Calvete, J.J. / Pineda-Lucena, A.
CitationJournal: Proteins / Year: 2011
Title: NMR Structure and Dynamics of Recombinant Wild-Type and Mutated Jerdostatin, a Selective Inhibitor of Integrin Alpha1 Beta1
Authors: Carbajo, R.J. / Sanz, L. / Mosulen, S. / Perez, A. / Marcinkiewicz, C. / Pineda-Lucena, A. / Calvete, J.J.
History
DepositionJan 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references / Version format compliance
Revision 1.2Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHORT DISINTEGRIN JERDOSTATIN


Theoretical massNumber of molelcules
Total (without water)4,9121
Polymers4,9121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 50LOWEST TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide SHORT DISINTEGRIN JERDOSTATIN / JERDOSTATIN


Mass: 4911.605 Da / Num. of mol.: 1 / Fragment: RESIDUES 68-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRIMERESURUS JERDONII (snake) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZZM2
Sequence detailsFIRST THREE RESIDUES (AMD) NOT PRESENT IN THE SEQUENCE DEPOSITED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
13115N HSQC
14113C HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR AND HETERONUCLEAR NMR SPECTROSCOPY ON 15N-LABELLED JERDOSTATIN

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Sample preparation

DetailsContents: 90% H2O / 10% D2O
Sample conditionsIonic strength: 0 / pH: 4.5 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 40

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